The present disclosure relates to a single-photon avalanche diode integrated with a quenching resistor and a manufacturing method thereof. The method includes: obtaining a wafer; patterning and etching a front surface of the base to form a quenching resistor trench and an isolation trench, wherein a width of the isolation trench is greater than a width of the quenching resistor trench; forming an insulation layer on an inner surface of the quenching resistor trench; depositing polycrystalline silicon on the front surface of the base, where the polycrystalline silicon is filled into the quenching resistor trench and seals the quenching resistor trench while the polycrystalline silicon is filled into the isolation trench and does not seal the isolation trench; performing oxidation treatment on the polycrystalline silicon in the isolation trench; filling a light-shielding conductive material into the isolation trench.